To hide marked items on picture just create copy of theme for your network merchants.
And in template files: 'destination.tpl' remove or comment by html comment <!-- commented -->
lines:
<tr><td>{widget id="D"}{widget id="DHelp" class="Inliner"}</td></tr>
<tr><td>{widget id="DPanel" class="DefaultLocation"}</td></tr>
(this remove option 'Replicated site is at default location', but merchant will need to second option to activate it, because this first was present value)
and in file: 'replicated_site_source_radio.tpl'
remove or comment lines
<tr><td>{widget id="L"}{widget id="LHelp" class="Inliner"}</td></tr>
<tr><td>{widget id="LPanel"}</td></tr>
(this will remove option 'Replicate local files')
After this is useful to set this theme as default for all PAN merchants and hide option for changing themes by removing permission 'Theme' - read, write